Alignments for a candidate for ilvE in Desulfobulbus mediterraneus DSM 13871

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvE in Desulfobulbus mediterraneus DSM 13871

Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_028585906.1 G494_RS0119800 branched-chain amino acid aminotransferase

Query= BRENDA::A0A2Z4MEX9
         (357 letters)



>NCBI__GCF_000429965.1:WP_028585906.1
          Length = 361

 Score =  404 bits (1039), Expect = e-117
 Identities = 197/345 (57%), Positives = 247/345 (71%)

Query: 11  EQKKEKPASDKLGFGVHFTDHMFTMDYTEGKGWHDPQIVPYSPLTLDPAAMVFHYGQAVF 70
           +Q K KPA DKLGFG  F+DHMF+M +   +GWH   I PY  L LDPAAMV HYGQA+F
Sbjct: 16  DQLKSKPAQDKLGFGQFFSDHMFSMKWNRKQGWHQAAIQPYRQLDLDPAAMVLHYGQAIF 75

Query: 71  EGLKAYRNQEGKVRLFRPDQNFKRMNRSLERMSMPLIDEEFMVEALKQLVAVDKEWIPTE 130
           EG+KAYR ++G++ LFRP  NF RMN S  RM MP   EE +++AL+ L+ +D+EW+P  
Sbjct: 76  EGMKAYRAEDGRILLFRPQDNFARMNLSAVRMCMPRFPEERVLQALRSLIYLDREWVPRS 135

Query: 131 SGQSLYIRPFVIATEPCFGVRASHTYKLVIVLSPVGAYYAGGMKPVKIYVENNYVRAVRG 190
            G SLYIRP +IATEP  G+RA+  Y+  I+  PVGAYYA G  P  IYVE+ YVRAV G
Sbjct: 136 EGASLYIRPTMIATEPMLGLRAAEEYQFFIIACPVGAYYAEGFNPTTIYVEDQYVRAVPG 195

Query: 191 GTGNAKVAGNYAGSLKAQVEAKEKGYEQVLWLDGVENKYIEEVGSMNVFFKVKGEVWTPA 250
           G G+AK AGNYA SLKAQ+ A++KGY QVLWLD  E+KYIEEVG+ N+FF +   + TP 
Sbjct: 196 GVGDAKTAGNYAASLKAQIAAQKKGYTQVLWLDAREHKYIEEVGTSNIFFMINDVLLTPP 255

Query: 251 LNGSILEGITRDSTIQLLKDWGIPVVEKRISMEDLHTAYVNGELEEAFGTGTAAVISPVG 310
           L GSIL GITRDS +QL +DW I V E+ IS++++ TA  NG L+E+FGTGTAAVI+PVG
Sbjct: 256 LEGSILPGITRDSVLQLARDWEIRVEERPISIDEIITASENGTLQESFGTGTAAVIAPVG 315

Query: 311 DLNWNGHQMIINGEKTGELTTRLYDEMTGIQYGDREDKFGWSVEV 355
           +L +    + IN   TG L  RLY+E+ GIQ+G R D   W V V
Sbjct: 316 ELCYKESSIQINQGTTGPLAKRLYEELQGIQFGSRADHHEWVVPV 360


Lambda     K      H
   0.317    0.136    0.406 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 384
Number of extensions: 12
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 357
Length of database: 361
Length adjustment: 29
Effective length of query: 328
Effective length of database: 332
Effective search space:   108896
Effective search space used:   108896
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate WP_028585906.1 G494_RS0119800 (branched-chain amino acid aminotransferase)
to HMM TIGR01123 (ilvE: branched-chain amino acid aminotransferase (EC 2.6.1.42))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR01123.hmm
# target sequence database:        /tmp/gapView.17653.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01123  [M=313]
Accession:   TIGR01123
Description: ilvE_II: branched-chain amino acid aminotransferase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                 Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     7e-130  418.5   0.0   8.1e-130  418.3   0.0    1.0  1  lcl|NCBI__GCF_000429965.1:WP_028585906.1  G494_RS0119800 branched-chain am


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000429965.1:WP_028585906.1  G494_RS0119800 branched-chain amino acid aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  418.3   0.0  8.1e-130  8.1e-130       1     313 []      48     360 ..      48     360 .. 0.99

  Alignments for each domain:
  == domain 1  score: 418.3 bits;  conditional E-value: 8.1e-130
                                 TIGR01123   1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeel 69 
                                               W++a ++++ +l ld++++vlhYgq++feG+kayR +dG+illfRp++n +R++ sa r+ +P+ +ee 
  lcl|NCBI__GCF_000429965.1:WP_028585906.1  48 WHQAAIQPYRQLDLDPAAMVLHYGQAIFEGMKAYRAEDGRILLFRPQDNFARMNLSAVRMCMPRFPEER 116
                                               ********************************************************************* PP

                                 TIGR01123  70 flealkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsif 138
                                               +l+al+ l+ +d++wvp  + +asLY+RP++iate+ lG +aa+ey f+++a+PvGaY+++g +p++i+
  lcl|NCBI__GCF_000429965.1:WP_028585906.1 117 VLQALRSLIYLDREWVPRSE-GASLYIRPTMIATEPMLGLRAAEEYQFFIIACPVGAYYAEGFNPTTIY 184
                                               *****************888.************************************************ PP

                                 TIGR01123 139 veteyvRaapkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelv 207
                                               ve++yvRa+p+G+G +k++GnYaasl+aq  a+++g+ +v++ld+ e+k+ieevG++nif++++d  l+
  lcl|NCBI__GCF_000429965.1:WP_028585906.1 185 VEDQYVRAVPGGVGDAKTAGNYAASLKAQIAAQKKGYTQVLWLDAREHKYIEEVGTSNIFFMIND-VLL 252
                                               *****************************************************************.9** PP

                                 TIGR01123 208 ttplsesiLegvtresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkieg 274
                                               t+pl +siL+g+tr+s+l+la+d+ ++veer i+ide+  a+e+G +   f++Gtaavi+Pvgel  ++
  lcl|NCBI__GCF_000429965.1:WP_028585906.1 253 TPPLEGSILPGITRDSVLQLARDWEIRVEERPISIDEIITASENGTLqeSFGTGTAAVIAPVGELCYKE 321
                                               *********************************************99999******************* PP

                                 TIGR01123 275 kevevkseevGevtkklrdeltdiqyGkledkegWivev 313
                                               ++++++++ +G+++k+l++el +iq+G+ +d+++W+v v
  lcl|NCBI__GCF_000429965.1:WP_028585906.1 322 SSIQINQGTTGPLAKRLYEELQGIQFGSRADHHEWVVPV 360
                                               ************************************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (313 nodes)
Target sequences:                          1  (361 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.62
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis